antspymm 1.3.5__py3-none-any.whl → 1.3.6__py3-none-any.whl

antspymm/mm.py

@@ -7979,14 +7979,13 @@ def mm_csv(
         t1wide.to_csv( hierfn + 'mmwide.csv' )
     ################# read the hierarchical data ###############################
     # over-write the rbp data with a consistent and recent approach ############
-    myx = antspyt1w.inspect_raw_t1( t1, hierfn + 'rbp' , option='both' ) 
+    myx = antspyt1w.inspect_raw_t1( t1, hierfn + 'rbp' , option='both' )
+    myx['brain'].to_csv( hierfn + 'rbp.csv', index=False )
+    myx['brain'].to_csv( hierfn + 'rbpbrain.csv', index=False )
     del myx
     hier = antspyt1w.read_hierarchical( hierfn )
-    if exists( hierfn + 'mmwide.csv' ) :
-        t1wide = pd.read_csv( hierfn + 'mmwide.csv' )
-    elif not testloop:
-        t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
-                hier['dataframes'], identifier=None )
+    t1wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
+        hier['dataframes'], identifier=None )
     rgrade = str( t1wide['resnetGrade'].iloc[0] )
     if t1wide['resnetGrade'].iloc[0] < 0.20:
         warnings.warn('T1w quality check indicates failure: ' + rgrade + " will not process." )
@@ -8087,6 +8086,8 @@ def mm_csv(
                 print( 'example image name is : '  )
                 print( myimgsr )
             if overmodX == 'NM2DMT':
+                dowrite = True
+                visualize = True
                 subjectpropath = os.path.dirname( mydoc['outprefix'] )
                 if verbose:
                     print("subjectpropath is")
@@ -8146,16 +8147,17 @@ def mm_csv(
                         print(f"antspymmerror occurred while processing {overmodX}: {e}")
                         pass
                     if not test_run:
-                        write_mm( output_prefix=mymm, mm=tabPro, mm_norm=normPro, t1wide=None, separator=mysep )
-                        nmpro = tabPro['NM']
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                    if visualize:
-                        mysl = range( nmpro['NM_avg'].shape[2] )
-                        ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
-                        mysl = range( nmpro['NM_avg_cropped'].shape[2] )
-                        ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
-                        ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
+                        if dowrite:
+                            write_mm( output_prefix=mymm, mm=tabPro,
+                                mm_norm=normPro, t1wide=None, separator=mysep )
+                        if visualize :
+                            nmpro = tabPro['NM']
+                            mysl = range( nmpro['NM_avg'].shape[2] )
+                            ants.plot( nmpro['NM_avg'],  nmpro['t1_to_NM'], slices=mysl, axis=2, title='nm + t1', filename=mymm+mysep+"NMavg.png" )
+                            mysl = range( nmpro['NM_avg_cropped'].shape[2] )
+                            ants.plot( nmpro['NM_avg_cropped'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop', filename=mymm+mysep+"NMavgcrop.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['t1_to_NM'], axis=2, slices=mysl, overlay_alpha=0.3, title='nm crop + t1', filename=mymm+mysep+"NMavgcropt1.png" )
+                            ants.plot( nmpro['NM_avg_cropped'], nmpro['NM_labels'], axis=2, slices=mysl, title='nm crop + labels', filename=mymm+mysep+"NMavgcroplabels.png" )
             else :
                 if len( myimgsr ) > 0:
                     dowrite=False

{antspymm-1.3.5.dist-info → antspymm-1.3.6.dist-info}/METADATA

@@ -1,18 +1,18 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.5
+Version: 1.3.6
 Summary: multi-channel/time-series medical image processing with antspyx
-Home-page: https://github.com/stnava/ANTsPyMM
-Author: Avants, Gosselin, Tustison, Reardon
-Author-email: stnava@gmail.com
+Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: h5py >=2.10.0
 Requires-Dist: numpy >=1.19.4
 Requires-Dist: pandas >=1.0.1
 Requires-Dist: antspyx
-Requires-Dist: antspyt1w >=0.2.3
+Requires-Dist: antspynet >=0.2.5
+Requires-Dist: antspyt1w >=0.9.3
 Requires-Dist: pathlib
 Requires-Dist: dipy
 Requires-Dist: nibabel
@@ -35,7 +35,7 @@ production environments.
 install the `dev` version by calling (within the source directory):
 
 ```
-python setup.py install
+python3 -m  build .
 ```
 
 or install the latest release via 
@@ -450,9 +450,12 @@ ssl._create_default_https_context = ssl._create_unverified_context
 
 ## to publish a release
 
+before doing this - make sure you have a recent run of `pip-compile pyproject.toml`
+
 ```
 rm -r -f build/ antspymm.egg-info/ dist/
-python3 setup.py sdist bdist_wheel
-twine upload --repository antspymm dist/*
+python3 -m  build .
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository antspymm dist/*
 ```
 

antspymm-1.3.6.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
+antspymm/mm.py,sha256=4g15BkmRyIn-ZTB7DOT9ggTDt-Ma3be44zKpCTALikY,479806
+antspymm-1.3.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.3.6.dist-info/METADATA,sha256=CRZs-L_1fv4rQPaKsMDPK0_9SHr6BLEyieHo30fLctw,14684
+antspymm-1.3.6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+antspymm-1.3.6.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.3.6.dist-info/RECORD,,

antspymm-1.3.5.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
-antspymm/mm.py,sha256=7UVUV4vASSwsASTT2aObJX4dg7mU28K4H85106BTuXM,479710
-antspymm-1.3.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.3.5.dist-info/METADATA,sha256=sJaL9YV5hUbe04k_j8YG0DhiNyyJc9CMBo-AdWDH6-M,14590
-antspymm-1.3.5.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-antspymm-1.3.5.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.3.5.dist-info/RECORD,,